Lauren Coombe

Low sum in ragoo.fasta

16

Hello, I am attempting to run Ragoo using a long-read assembly as the 'reference'. After running Ragoo with the following command: ``` ragoo.py -t 4 -b -C ${assembly} ${ref} ```...

ntlink 1.3.4

1

- [x] Have you followed the [guidelines for contributing](https://github.com/brewsci/homebrew-bio/blob/master/CONTRIBUTING.md)? - [x] Have you checked that there aren't other open [pull requests](https://github.com/brewsci/homebrew-bio/pulls) for the same formula update/change? - [x] Have you...

Update btllib to 1.4.8

1

Update btllib to 1.4.8 ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). * If this PR adds or updates a recipe, use "Add" or...

Hello all, As we discussed via Slack, I found that the phred quality scores when outputting perfect reads appear to vary as expected for when simulating error reads, instead of...

Unexpected mashtree parameters for bootstrap replicates

1

**Describe the bug** It looks like some `mashtree` parameters such as `--kmerlength` and `--sketch-size` are not propagated to `mash sketch` when running the bootstrap replicates. **To Reproduce** Steps to reproduce...

Since we added indexlr to the `recipes` directory, would also make sense to add `long-to-linked-pe` - there are currently copies of that code in ARCS and Tigmint

Currently, to compute minimizers with the python wrapper for indexlr, the sequences need to be in a file on disk. Ideally (if possible), there would also be an option to...

* Ie. target in `goldrush` makefile to skip the polishing step, in the case the user might want that flexibility

**Snakemake version** version 8.17.0 **Describe the bug** When I run my previously functional snakemake file, I get a ValueError: ``` ValueError: Invalid config definition: Config entry must start with a...